├── .gitignore ├── generated_scripts ├── ps103f.sh └── ps103f_varTMT.sh ├── .bashrc ├── LICENSE ├── README.md ├── gen_mqpar.py └── templates ├── SILAC.xml ├── SILAC_varTMT.xml ├── yeast_labelfree.xml ├── labelfree.xml └── TMT_11plex.xml /.gitignore: -------------------------------------------------------------------------------- 1 | # sublime files 2 | *.sublime-project 3 | *.sublime-workspace 4 | 5 | # OS files 6 | desktop.ini 7 | .DS_Store 8 | 9 | -------------------------------------------------------------------------------- /generated_scripts/ps103f.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | #SBATCH --job-name=fp103f 3 | #SBATCH --output=fp103f.out 4 | #SBATCH --ntasks=1 5 | #SBATCH --cpus-per-task=16 6 | #SBATCH --mem-per-cpu=1000 7 | #SBATCH --time=24:0:0 8 | #SBATCH --partition=general 9 | 10 | source /home/chen.alb/.bashrc 11 | srun mono $MQ_1_6_3_3 /home/chen.alb/fp103f.xml 12 | -------------------------------------------------------------------------------- /generated_scripts/ps103f_varTMT.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | #SBATCH --job-name=fp103f_varTMT 3 | #SBATCH --output=fp103f_varTMT.out 4 | #SBATCH --ntasks=1 5 | #SBATCH --cpus-per-task=16 6 | #SBATCH --mem-per-cpu=1000 7 | #SBATCH --time=24:0:0 8 | #SBATCH --partition=general 9 | 10 | source /home/chen.alb/.bashrc 11 | srun mono $MQ_1_6_3_3 /home/chen.alb/fp103f_varTMT.xml 12 | -------------------------------------------------------------------------------- /.bashrc: -------------------------------------------------------------------------------- 1 | # .bashrc 2 | 3 | # Source global definitions 4 | if [ -f /etc/bashrc ]; then 5 | . /etc/bashrc 6 | fi 7 | 8 | 9 | # User specific aliases and functions 10 | 11 | SCRATCH=/scratch/chen.alb 12 | SC=/scratch/chen.alb 13 | 14 | MQ_1_6_2_3=~/MQ_1.6.2.3/bin/MaxQuantCmd.exe 15 | MQ_1_6_2_10=~/MQ_1.6.2.10/bin/MaxQuantCmd.exe 16 | MQ_1_6_3_2=~/MQ_1.6.3.2/bin/MaxQuantCmd.exe 17 | MQ_1_6_3_3=~/MQ_1.6.3.3/bin/MaxQuantCmd.exe 18 | 19 | 20 | # load slurm modules 21 | module load legacy/2018-05-18 22 | module load openmpi/3.1.2 23 | module load gcc/8.1.0 24 | module load python/3.7.0 25 | module load anaconda3/3.7 26 | module load matlab/R2018a 27 | 28 | module load mono-5.10.1.47 29 | module load git-2.9.5 30 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2019 Albert Chen 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | MaxQuant for Linux Guide 2 | ======================== 3 | 4 | Read my blog post here: [http://atchen.me/research/2019/03/21/mq-linux.html](http://atchen.me/research/2019/03/21/mq-linux.html) 5 | 6 | The goal of the `gen_mqpar.py` script is to create MaxQuant configuration files (`mqpar.xml` files) in a console environment without having to transfer one over or edit the XML manually. The example given has some hard-coded stuff and makes assumptions about your filesystem, so please follow the steps below to get started. 7 | 8 | 1. Verify that [Mono](https://www.mono-project.com/download/stable/#download-lin) is installed. 9 | 10 | Note, If searching Bruker timsTOF data, you need `gcc` version 8.3+. Check the version with `gcc --version`. You can install gcc8 with these commands: 11 | 12 | ```bash 13 | # For CentOS 7: 14 | 15 | yum install centos-release-scl 16 | yum install devtoolset-8 17 | scl enable devtoolset-8 -- bash 18 | 19 | # Enable the tools (put this into .bash_profile) 20 | source /opt/rh/devtoolset-8/enable 21 | ``` 22 | 23 | (Thanks to [@cscaife](https://github.com/cscaife) for identifying this step, and [https://stackoverflow.com/a/55876012](https://stackoverflow.com/a/55876012) for the install instructions) 24 | 25 | 2. Create template `mqpar.xml` files – representing configurations for MaxQuant searches you routinely run on your experiments. I put a bunch of my templates in a folder, `templates/` for easy access. 26 | - I recommend generating these first in the MaxQuant GUI, as it's easier and you can verify that the configuration file is valid before moving it to your Linux instance. 27 | - Don't worry about the raw files, folder paths, or FASTA file paths in the template file – they will be replaced by the script 28 | 3. Move the MaxQuant files onto your Linux instance. My setup has MaxQuant versions separately in a folder `MQ/`, i.e., `MQ/MaxQuant_1_7_0`. I then map this path to an environment variable in my `.bash_profile`, with `export MQ_1_7_0=~/MQ_1_7_0/bin/MaxQuantCmd.exe`. You can manage your MaxQuant versions however you like, just make sure that it's reflected in the `gen_mqpar.py` script. 29 | 4. Move your protein FASTA files over to the Linux instance. The current `gen_mqpar.py` script has the path to the FASTA file hard-coded, and it's straightforward to change this or make it argument-driven. 30 | 31 | Run: 32 | ```bash 33 | ./gen_mqpar.py -o -t 34 | # for example, 35 | ./gen_mqpar.py templates/SILAC.xml raw_files/FP93 -o fp93_silac.xml -t 6 36 | 37 | ``` 38 | 39 | If you're getting errors with starting MaxQuant with the generated `mqpar` files, then I would manually check all of the paths in the XML file first. 40 | 41 | -------------------------------------------------------------------------------- /gen_mqpar.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | #coding: utf-8 3 | 4 | import argparse 5 | import os 6 | import sys 7 | import re 8 | import time 9 | 10 | parser = argparse.ArgumentParser(description='MaxQuant fun') 11 | parser.add_argument('input_xml', type=argparse.FileType('r', encoding='UTF-8')) 12 | parser.add_argument('raw_file_folders', type=str, nargs='+') 13 | parser.add_argument('-o', '--outfile', type=str, required=True) 14 | parser.add_argument('-mq', '--mq-version', type=str, default='1_6_3_3', choices=['1_6_2_3', '1_6_2_10', '1_6_3_2', '1_6_3_3'], help='MaxQuant version') 15 | parser.add_argument('-t', '--threads', type=int, default=4, help='Number of threads to specify in MaxQuant configuration file') 16 | 17 | args = parser.parse_args() 18 | 19 | mqpar = open(args.input_xml.name, 'r') 20 | mqpar_text = mqpar.read() 21 | mqpar.close() 22 | 23 | 24 | # replace fasta path 25 | fasta_path = '/home/chen.alb/FASTA/swissprot_human_20180730.fasta' 26 | fasta_path = ('' + fasta_path + '') 27 | mqpar_text = re.sub(r'\(.|\n|\r)*\<\/fastaFilePath\>', fasta_path, mqpar_text) 28 | 29 | file_counter = 0 30 | file_path_repl_text = '\n' 31 | 32 | for folder in args.raw_file_folders: 33 | files = [f for f in os.listdir(folder) if os.path.isfile(os.path.join(folder, f))] 34 | # only take raw files 35 | files = [f for f in files if f[-4:] == '.raw'] 36 | 37 | for file in files: 38 | file_path_repl_text += ('' + os.path.join(folder, file) + '\n') 39 | file_counter += 1 40 | 41 | file_path_repl_text += '' 42 | 43 | 44 | 45 | mqpar_text = re.sub(r'\(.|\n|\r)*\<\/filePaths\>', file_path_repl_text, mqpar_text) 46 | 47 | # change experiments, fractions, ptms, paramGroupIndices to reflect # of raw files added 48 | experiments_text = '\n' 49 | fractions_text = '\n' 50 | ptms_text = '\n' 51 | group_inds_text = '\n' 52 | reference_channels_text = '\n' 53 | 54 | for i in range(0, file_counter): 55 | experiments_text += '\n' 56 | fractions_text += '32767\n' 57 | ptms_text += 'False\n' 58 | group_inds_text += '0\n' 59 | reference_channels_text += '\n' 60 | 61 | experiments_text += '\n' 62 | fractions_text += '\n' 63 | ptms_text += '\n' 64 | group_inds_text += '\n' 65 | reference_channels_text += '' 66 | 67 | mqpar_text = re.sub(r'\(.|\n|\r)*\<\/referenceChannel\>', \ 68 | experiments_text+fractions_text+ptms_text+group_inds_text+reference_channels_text, mqpar_text) 69 | 70 | 71 | # ok, instead, name the output folder after the named xml output 72 | output_folder = os.path.basename(args.outfile) 73 | # remove the .xml, if it exists 74 | output_folder = re.sub(r'\.xml', '', output_folder) 75 | # remove the beginning "mqpar_", if it exists 76 | output_folder = re.sub(r'mqpar_', '', output_folder) 77 | # append the scratch folder 78 | output_folder = ('/scratch/chen.alb/' + output_folder) 79 | 80 | # create the folder 81 | if not os.path.exists(output_folder): 82 | os.makedirs(output_folder) 83 | 84 | # add xml around 85 | mqpar_text = re.sub(r'\(.|\n|\r)*\<\/fixedCombinedFolder\>',\ 86 | ('' + output_folder + ''), mqpar_text) 87 | 88 | # replace andromeda index -- folder inside of the output folder 89 | andromeda_index_path = os.path.join(output_folder, 'andromeda_index') 90 | andromeda_index_path = ('' + andromeda_index_path + '') 91 | mqpar_text = re.sub(r'\(.|\n|\r)*\<\/fixedSearchFolder\>', andromeda_index_path, mqpar_text) 92 | 93 | # replace temp folder -- folder inside of the output folder 94 | 95 | temp_path = os.path.join(output_folder, 'temp') 96 | temp_path = ('' + temp_path + '') 97 | mqpar_text = re.sub(r'\(.|\n|\r)*\<\/tempFolder\>', temp_path, mqpar_text) 98 | 99 | # replace number of threads 100 | threads_tag = ('' + str(args.threads) + '') 101 | mqpar_text = re.sub(r'\(.|\n|\r)*\<\/numThreads\>', threads_tag, mqpar_text) 102 | 103 | 104 | ### create the slurm script 105 | slurm_script = ('#!/bin/sh\n' 106 | '#SBATCH --job-name={JOBNAME}\n' 107 | '#SBATCH --output={JOBNAME}.out\n' 108 | '#SBATCH --ntasks=1\n' 109 | '#SBATCH --cpus-per-task=16\n' 110 | '#SBATCH --mem-per-cpu=1000\n' 111 | '#SBATCH --time=24:0:0\n' 112 | '#SBATCH --partition=general\n\n' 113 | 'source /home/chen.alb/.bashrc\n' 114 | 'srun mono ${MQ_VERSION} {MQPAR}\n' 115 | ) 116 | # replace variables in the slurm script 117 | slurm_script = re.sub(r'{MQ_VERSION}', ('MQ_' + args.mq_version), slurm_script) 118 | slurm_script = re.sub(r'{MQPAR}', os.path.abspath(args.outfile), slurm_script) 119 | slurm_script = re.sub(r'{JOBNAME}', os.path.basename(output_folder), slurm_script) 120 | 121 | # write slurm script - same format as the output folder 122 | slurm_script_path = os.path.join(os.path.expanduser('~'), 'scripts', os.path.basename(output_folder)) + '.sh' 123 | slurm_script_file = open(slurm_script_path, 'w') 124 | slurm_script_file.write(slurm_script) 125 | slurm_script_file.close() 126 | 127 | # write XML file 128 | out_file = open(args.outfile, 'w') 129 | out_file.write(mqpar_text) 130 | out_file.close() 131 | print('success!') 132 | -------------------------------------------------------------------------------- /templates/SILAC.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | /home/chen.alb/FASTA/swissprot_human_20180730.fasta 6 | >([^\s]*) 7 | >(.*) 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | /scratch/chen.alb/asdf/andromeda_index 19 | 350000 20 | True 21 | 0.005 22 | False 23 | False 24 | False 25 | False 26 | True 27 | True 28 | revert 29 | all 30 | True 31 | 4600 32 | True 33 | True 34 | True 35 | 0 36 | 6 37 | 0 38 | 40 39 | True 40 | False 41 | False 42 | False 43 | False 44 | 0 45 | 0 46 | False 47 | False 48 | False 49 | False 50 | 0 51 | False 52 | False 53 | False 54 | False 55 | False 56 | False 57 | Species 58 | False 59 | 3 60 | False 61 | True 62 | False 63 | True 64 | False 65 | False 66 | 67 | 68 | 69 | 7 70 | 0.01 71 | 1 72 | 1 73 | 0.01 74 | 8 75 | 25 76 | True 77 | 1 78 | 1 79 | 0 80 | False 81 | True 82 | False 83 | 84 | 2 85 | True 86 | 87 | Oxidation (M) 88 | Acetyl (Protein N-term) 89 | 90 | 0 91 | 0 92 | 25 93 | 15 94 | 0 95 | 1 96 | 97 | 98 | 200 99 | True 100 | True 101 | True 102 | True 103 | True 104 | True 105 | True 106 | False 107 | False 108 | False 109 | True 110 | False 111 | True 112 | 0.8 113 | 0.9 114 | 1 115 | False 116 | 0 117 | 20 118 | 119 | none 120 | False 121 | session1 122 | 1.6.3.3 123 | /scratch/chen.alb/asdf/temp 124 | 125 | 8 126 | 127 | 128 | 129 | /scratch/chen.alb/asdf 130 | -1.79589544172745E+308 131 | 1.79589544172745E+308 132 | False 133 | False 134 | False 135 | True 136 | False 137 | False 138 | False 139 | 140 | /scratch/chen.alb/FP86/181001S_X_FP86D.raw 141 | /scratch/chen.alb/FP86/181001S_X_FP86B.raw 142 | 143 | 144 | 145 | 146 | 147 | 148 | 32767 149 | 32767 150 | 151 | 152 | False 153 | False 154 | 155 | 156 | 0 157 | 0 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 0 166 | 7 167 | 2 168 | False 169 | False 170 | True 171 | 1 172 | NaN 173 | NaN 174 | MatchFromAndTo 175 | 0 176 | 8 177 | True 178 | 35 179 | True 180 | 1.4 181 | 1.2 182 | False 183 | 0 184 | 185 | 186 | Arg10;Lys8 187 | 188 | Standard 189 | False 190 | 0 191 | False 192 | 3 193 | 6 194 | 100000 195 | 0 196 | 0 197 | False 198 | False 199 | True 200 | False 201 | 2 202 | 3 203 | 5 204 | 2 205 | 2 206 | 0 207 | 0 208 | 0 209 | 0 210 | 211 | 212 | 213 | Trypsin/P 214 | 215 | 216 | 217 | 0 218 | False 219 | False 220 | 221 | Oxidation (M) 222 | Acetyl (Protein N-term) 223 | 224 | False 225 | 226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | False 234 | 235 | 236 | 237 | 238 | True 239 | 20 240 | 4.5 241 | True 242 | 2 243 | True 244 | 0.6 245 | 0.6 246 | True 247 | True 248 | False 249 | 70 250 | False 251 | 252 | 0 253 | 0 254 | 0 255 | NaN 256 | NaN 257 | False 258 | NaN 259 | NaN 260 | 0 261 | 0 262 | 0 263 | 0 264 | True 265 | False 266 | True 267 | False 268 | 269 | 0 270 | 6 271 | False 272 | 0 273 | 0 274 | 0 275 | 0 276 | False 277 | 278 | 279 | 280 | 281 | PeptidesWithCleavedLinker 282 | False 283 | True 284 | 285 | 286 | 287 | 288 | FTMS 289 | 20 290 | True 291 | 7 292 | True 293 | 10 294 | True 295 | True 296 | 12 297 | 100 298 | True 299 | True 300 | True 301 | True 302 | False 303 | 304 | 305 | ITMS 306 | 0.5 307 | False 308 | 0.15 309 | False 310 | 0.25 311 | False 312 | False 313 | 8 314 | 100 315 | True 316 | True 317 | True 318 | True 319 | False 320 | 321 | 322 | TOF 323 | 40 324 | True 325 | 0.01 326 | False 327 | 0.02 328 | False 329 | True 330 | 10 331 | 100 332 | True 333 | True 334 | True 335 | True 336 | False 337 | 338 | 339 | Unknown 340 | 0.5 341 | False 342 | 0.15 343 | False 344 | 0.25 345 | False 346 | False 347 | 8 348 | 100 349 | True 350 | True 351 | True 352 | True 353 | False 354 | 355 | 356 | 357 | -------------------------------------------------------------------------------- /templates/SILAC_varTMT.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | /home/chen.alb/FASTA/swissprot_human_20180730.fasta 6 | >([^\s]*) 7 | >(.*) 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | /scratch/chen.alb/asdf/andromeda_index 19 | 350000 20 | True 21 | 0.005 22 | False 23 | False 24 | False 25 | False 26 | True 27 | True 28 | revert 29 | all 30 | True 31 | 4600 32 | True 33 | True 34 | True 35 | 0 36 | 6 37 | 0 38 | 40 39 | True 40 | False 41 | False 42 | False 43 | False 44 | 0 45 | 0 46 | False 47 | False 48 | False 49 | False 50 | 0 51 | False 52 | False 53 | False 54 | False 55 | False 56 | False 57 | Species 58 | False 59 | 3 60 | False 61 | True 62 | False 63 | True 64 | False 65 | False 66 | 67 | 68 | 69 | 7 70 | 0.01 71 | 1 72 | 1 73 | 0.01 74 | 8 75 | 25 76 | True 77 | 1 78 | 1 79 | 0 80 | False 81 | True 82 | False 83 | 84 | 2 85 | True 86 | 87 | Oxidation (M) 88 | Acetyl (Protein N-term) 89 | Phospho (STY) 90 | 91 | 0 92 | 0 93 | 25 94 | 15 95 | 0 96 | 1 97 | 98 | 99 | 200 100 | True 101 | True 102 | True 103 | True 104 | True 105 | True 106 | True 107 | False 108 | False 109 | False 110 | True 111 | False 112 | True 113 | 0.8 114 | 0.9 115 | 1 116 | False 117 | 0 118 | 20 119 | 120 | none 121 | False 122 | session1 123 | 1.6.2.10 124 | /scratch/chen.alb/asdf/temp 125 | 126 | 8 127 | 128 | 129 | 130 | /scratch/chen.alb/asdf 131 | -1.79589544172745E+308 132 | 1.79589544172745E+308 133 | False 134 | False 135 | False 136 | True 137 | False 138 | False 139 | False 140 | 141 | /scratch/chen.alb/FP86/181001S_X_FP86D.raw 142 | 143 | 144 | 145 | 146 | 147 | 32767 148 | 149 | 150 | False 151 | 152 | 153 | 0 154 | 155 | 156 | 157 | 158 | 159 | 160 | 0 161 | 7 162 | 2 163 | False 164 | False 165 | True 166 | 1 167 | NaN 168 | NaN 169 | MatchFromAndTo 170 | 0 171 | 8 172 | True 173 | 35 174 | True 175 | 1.4 176 | 1.2 177 | False 178 | 0 179 | 180 | 181 | Arg10;Lys8 182 | 183 | Standard 184 | False 185 | 0 186 | False 187 | 3 188 | 6 189 | 100000 190 | 0 191 | 0 192 | False 193 | False 194 | True 195 | False 196 | 2 197 | 3 198 | 5 199 | 2 200 | 2 201 | 0 202 | 0 203 | 0 204 | 0 205 | 206 | 207 | 208 | Trypsin/P 209 | 210 | 211 | 212 | 0 213 | False 214 | False 215 | 216 | Oxidation (M) 217 | Acetyl (Protein N-term) 218 | Phospho (STY) DHP Neutral Losses 219 | TMT10plex-Lys Modification 220 | TMT10plex-Nter-Modification 221 | 222 | False 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | 231 | False 232 | 233 | 234 | 235 | 236 | True 237 | 20 238 | 4.5 239 | True 240 | 2 241 | True 242 | 0.6 243 | 0.6 244 | True 245 | True 246 | False 247 | 70 248 | False 249 | 250 | 0 251 | 0 252 | 0 253 | NaN 254 | NaN 255 | False 256 | NaN 257 | NaN 258 | 0 259 | 0 260 | 0 261 | 0 262 | True 263 | False 264 | True 265 | False 266 | 267 | 0 268 | 6 269 | False 270 | 0 271 | 0 272 | 0 273 | 0 274 | False 275 | 276 | 277 | 278 | 279 | PeptidesWithCleavedLinker 280 | False 281 | True 282 | 283 | 284 | 285 | 286 | FTMS 287 | 20 288 | True 289 | 7 290 | True 291 | 10 292 | True 293 | True 294 | 12 295 | 100 296 | True 297 | True 298 | True 299 | True 300 | False 301 | 302 | 303 | ITMS 304 | 0.5 305 | False 306 | 0.15 307 | False 308 | 0.25 309 | False 310 | False 311 | 8 312 | 100 313 | True 314 | True 315 | True 316 | True 317 | False 318 | 319 | 320 | TOF 321 | 40 322 | True 323 | 0.01 324 | False 325 | 0.02 326 | False 327 | True 328 | 10 329 | 100 330 | True 331 | True 332 | True 333 | True 334 | False 335 | 336 | 337 | Unknown 338 | 0.5 339 | False 340 | 0.15 341 | False 342 | 0.25 343 | False 344 | False 345 | 8 346 | 100 347 | True 348 | True 349 | True 350 | True 351 | False 352 | 353 | 354 | 355 | -------------------------------------------------------------------------------- /templates/yeast_labelfree.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | C:\Users\nslavov\Desktop\swissprot_human_20180730.fasta 6 | >([^\s]*) 7 | >(.*) 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | D:\andromeda_index 19 | 350000 20 | True 21 | 0.005 22 | False 23 | False 24 | False 25 | False 26 | True 27 | True 28 | revert 29 | all 30 | True 31 | 4600 32 | True 33 | True 34 | True 35 | 0 36 | 6 37 | 0 38 | 40 39 | True 40 | False 41 | False 42 | False 43 | False 44 | 0 45 | 0 46 | False 47 | False 48 | False 49 | False 50 | 0 51 | False 52 | False 53 | False 54 | False 55 | False 56 | False 57 | Species 58 | False 59 | 3 60 | False 61 | True 62 | False 63 | True 64 | False 65 | False 66 | 67 | 68 | 69 | 7 70 | 0.01 71 | 1 72 | 1 73 | 0.01 74 | 8 75 | 25 76 | True 77 | 1 78 | 1 79 | 0 80 | False 81 | True 82 | False 83 | 84 | 2 85 | True 86 | 87 | Oxidation (M) 88 | Acetyl (Protein N-term) 89 | 90 | 0 91 | 0 92 | 25 93 | 15 94 | 0 95 | 1 96 | 97 | 98 | 200 99 | True 100 | True 101 | True 102 | True 103 | True 104 | True 105 | True 106 | False 107 | False 108 | True 109 | False 110 | True 111 | False 112 | 0 113 | 20 114 | 115 | none 116 | False 117 | session1 118 | 1.6.3.3 119 | D:\tmp 120 | 121 | 6 122 | 123 | 124 | 125 | D:\MQ_Out 126 | -1.79769313486232E+308 127 | 1.79769313486232E+308 128 | False 129 | False 130 | False 131 | True 132 | False 133 | False 134 | False 135 | 136 | D:\Raw Files\MS3\tkF181029_Albert_TMT_10x_MS3.raw 137 | 138 | 139 | 140 | 141 | 142 | 32767 143 | 144 | 145 | False 146 | 147 | 148 | 0 149 | 150 | 151 | 152 | 153 | 154 | 155 | 0 156 | 7 157 | 2 158 | False 159 | False 160 | True 161 | 1 162 | NaN 163 | NaN 164 | MatchFromAndTo 165 | 0 166 | 8 167 | True 168 | 35 169 | True 170 | 1.4 171 | 1.2 172 | False 173 | 0 174 | 175 | 176 | 177 | Standard 178 | False 179 | 0 180 | False 181 | 3 182 | 6 183 | 100000 184 | 0 185 | 0 186 | False 187 | False 188 | True 189 | False 190 | 2 191 | 0 192 | 5 193 | 2 194 | 1 195 | 0 196 | 0 197 | 0 198 | 0 199 | 200 | 201 | 202 | Trypsin/P 203 | LysC/P 204 | 205 | 206 | 207 | 0 208 | False 209 | False 210 | 211 | Oxidation (M) 212 | Acetyl (Protein N-term) 213 | 214 | False 215 | 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | False 224 | 225 | 226 | 227 | 228 | True 229 | 20 230 | 4.5 231 | True 232 | 2 233 | True 234 | 0.6 235 | 0.6 236 | True 237 | True 238 | False 239 | 70 240 | False 241 | 242 | 0 243 | 0 244 | 0 245 | NaN 246 | NaN 247 | False 248 | NaN 249 | NaN 250 | 0 251 | 0 252 | 0 253 | 0 254 | True 255 | False 256 | True 257 | False 258 | 259 | 0 260 | 6 261 | False 262 | 0 263 | 0 264 | 0 265 | 0 266 | False 267 | 268 | 269 | 270 | 271 | PeptidesWithCleavedLinker 272 | False 273 | True 274 | 275 | 276 | 277 | 278 | FTMS 279 | 20 280 | True 281 | 7 282 | True 283 | 10 284 | True 285 | True 286 | 12 287 | 100 288 | True 289 | True 290 | True 291 | True 292 | False 293 | 294 | 295 | ITMS 296 | 0.5 297 | False 298 | 0.15 299 | False 300 | 0.25 301 | False 302 | False 303 | 8 304 | 100 305 | True 306 | True 307 | True 308 | True 309 | False 310 | 311 | 312 | TOF 313 | 40 314 | True 315 | 0.01 316 | False 317 | 0.02 318 | False 319 | True 320 | 10 321 | 100 322 | True 323 | True 324 | True 325 | True 326 | False 327 | 328 | 329 | Unknown 330 | 0.5 331 | False 332 | 0.15 333 | False 334 | 0.25 335 | False 336 | False 337 | 8 338 | 100 339 | True 340 | True 341 | True 342 | True 343 | False 344 | 345 | 346 | 347 | 348 | CID 349 | False 350 | 1 351 | 1 352 | 1 353 | False 354 | 1 355 | KRH 356 | 357 | 358 | HCD 359 | False 360 | 1 361 | 1 362 | 1 363 | False 364 | 1 365 | KRH 366 | 367 | 368 | ETD 369 | False 370 | 1 371 | 1 372 | 1 373 | False 374 | 1 375 | KRH 376 | 377 | 378 | PQD 379 | False 380 | 1 381 | 1 382 | 1 383 | False 384 | 1 385 | KRH 386 | 387 | 388 | ETHCD 389 | False 390 | 1 391 | 1 392 | 1 393 | False 394 | 1 395 | KRH 396 | 397 | 398 | ETCID 399 | False 400 | 1 401 | 1 402 | 1 403 | False 404 | 1 405 | KRH 406 | 407 | 408 | UVPD 409 | False 410 | 1 411 | 1 412 | 1 413 | False 414 | 1 415 | KRH 416 | 417 | 418 | Unknown 419 | False 420 | 1 421 | 1 422 | 1 423 | False 424 | 1 425 | KRH 426 | 427 | 428 | 429 | -------------------------------------------------------------------------------- /templates/labelfree.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | C:\Users\nslavov\Desktop\swissprot_human_20180730.fasta 6 | >([^\s]*) 7 | >(.*) 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | D:\andromeda_index 19 | 350000 20 | True 21 | 0.005 22 | False 23 | False 24 | False 25 | False 26 | True 27 | True 28 | revert 29 | all 30 | True 31 | 4600 32 | True 33 | True 34 | True 35 | 0 36 | 6 37 | 0 38 | 40 39 | True 40 | False 41 | False 42 | False 43 | False 44 | 0 45 | 0 46 | False 47 | False 48 | False 49 | False 50 | 0 51 | False 52 | False 53 | False 54 | False 55 | False 56 | False 57 | Species 58 | False 59 | 3 60 | False 61 | True 62 | False 63 | True 64 | False 65 | False 66 | 67 | 68 | 69 | 7 70 | 0.01 71 | 1 72 | 1 73 | 0.01 74 | 8 75 | 25 76 | True 77 | 1 78 | 1 79 | 0 80 | False 81 | True 82 | False 83 | 84 | 2 85 | True 86 | 87 | Oxidation (M) 88 | Acetyl (Protein N-term) 89 | 90 | 0 91 | 0 92 | 25 93 | 15 94 | 0 95 | 1 96 | 97 | 98 | 200 99 | True 100 | True 101 | True 102 | True 103 | True 104 | True 105 | True 106 | False 107 | False 108 | True 109 | False 110 | True 111 | False 112 | 0 113 | 20 114 | 115 | none 116 | False 117 | session1 118 | 1.6.3.3 119 | D:\tmp 120 | 121 | 6 122 | 123 | 124 | 125 | D:\MQ_Out 126 | -1.79769313486232E+308 127 | 1.79769313486232E+308 128 | False 129 | False 130 | False 131 | True 132 | False 133 | False 134 | False 135 | 136 | D:\Raw Files\MS3\tkF181029_Albert_TMT_10x_MS3.raw 137 | D:\Raw Files\MS3\tkF181029_Albert_TMT_10x_MStage.raw 138 | D:\Raw Files\MS3\tkF181029_Albert_TMT_10x_NL_01.raw 139 | D:\Raw Files\MS3\tkF181029_Albert_TMT_10x_NL_02.raw 140 | D:\Raw Files\MS3\tkF181029_Albert_TMT_10x_NL_CE45.raw 141 | D:\Raw Files\MS3\tkF181029_Albert_TMT_10x_NL_CE60.raw 142 | 143 | 144 | 145 | 146 | 147 | 148 | 149 | 150 | 151 | 152 | 32767 153 | 32767 154 | 32767 155 | 32767 156 | 32767 157 | 32767 158 | 159 | 160 | False 161 | False 162 | False 163 | False 164 | False 165 | False 166 | 167 | 168 | 0 169 | 0 170 | 0 171 | 0 172 | 0 173 | 0 174 | 175 | 176 | 177 | 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 0 186 | 7 187 | 2 188 | False 189 | False 190 | True 191 | 1 192 | NaN 193 | NaN 194 | MatchFromAndTo 195 | 0 196 | 8 197 | True 198 | 35 199 | True 200 | 1.4 201 | 1.2 202 | False 203 | 0 204 | 205 | 206 | 207 | Standard 208 | False 209 | 0 210 | False 211 | 3 212 | 6 213 | 100000 214 | 0 215 | 0 216 | False 217 | False 218 | True 219 | False 220 | 2 221 | 0 222 | 5 223 | 2 224 | 1 225 | 0 226 | 0 227 | 0 228 | 0 229 | 230 | 231 | 232 | Trypsin/P 233 | 234 | 235 | 236 | 0 237 | False 238 | False 239 | 240 | Oxidation (M) 241 | Acetyl (Protein N-term) 242 | 243 | False 244 | 245 | 246 | 247 | 248 | 249 | 250 | 251 | 252 | False 253 | 254 | 255 | 256 | 257 | True 258 | 20 259 | 4.5 260 | True 261 | 2 262 | True 263 | 0.6 264 | 0.6 265 | True 266 | True 267 | False 268 | 70 269 | False 270 | 271 | 0 272 | 0 273 | 0 274 | NaN 275 | NaN 276 | False 277 | NaN 278 | NaN 279 | 0 280 | 0 281 | 0 282 | 0 283 | True 284 | False 285 | True 286 | False 287 | 288 | 0 289 | 6 290 | False 291 | 0 292 | 0 293 | 0 294 | 0 295 | False 296 | 297 | 298 | 299 | 300 | PeptidesWithCleavedLinker 301 | False 302 | True 303 | 304 | 305 | 306 | 307 | FTMS 308 | 20 309 | True 310 | 7 311 | True 312 | 10 313 | True 314 | True 315 | 12 316 | 100 317 | True 318 | True 319 | True 320 | True 321 | False 322 | 323 | 324 | ITMS 325 | 0.5 326 | False 327 | 0.15 328 | False 329 | 0.25 330 | False 331 | False 332 | 8 333 | 100 334 | True 335 | True 336 | True 337 | True 338 | False 339 | 340 | 341 | TOF 342 | 40 343 | True 344 | 0.01 345 | False 346 | 0.02 347 | False 348 | True 349 | 10 350 | 100 351 | True 352 | True 353 | True 354 | True 355 | False 356 | 357 | 358 | Unknown 359 | 0.5 360 | False 361 | 0.15 362 | False 363 | 0.25 364 | False 365 | False 366 | 8 367 | 100 368 | True 369 | True 370 | True 371 | True 372 | False 373 | 374 | 375 | 376 | 377 | CID 378 | False 379 | 1 380 | 1 381 | 1 382 | False 383 | 1 384 | KRH 385 | 386 | 387 | HCD 388 | False 389 | 1 390 | 1 391 | 1 392 | False 393 | 1 394 | KRH 395 | 396 | 397 | ETD 398 | False 399 | 1 400 | 1 401 | 1 402 | False 403 | 1 404 | KRH 405 | 406 | 407 | PQD 408 | False 409 | 1 410 | 1 411 | 1 412 | False 413 | 1 414 | KRH 415 | 416 | 417 | ETHCD 418 | False 419 | 1 420 | 1 421 | 1 422 | False 423 | 1 424 | KRH 425 | 426 | 427 | ETCID 428 | False 429 | 1 430 | 1 431 | 1 432 | False 433 | 1 434 | KRH 435 | 436 | 437 | UVPD 438 | False 439 | 1 440 | 1 441 | 1 442 | False 443 | 1 444 | KRH 445 | 446 | 447 | Unknown 448 | False 449 | 1 450 | 1 451 | 1 452 | False 453 | 1 454 | KRH 455 | 456 | 457 | 458 | -------------------------------------------------------------------------------- /templates/TMT_11plex.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | C:\Users\nslavov\Desktop\swissprot_human_20180730.fasta 6 | >([^\s]*) 7 | >(.*) 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 350000 20 | True 21 | 0.005 22 | False 23 | False 24 | False 25 | False 26 | True 27 | True 28 | revert 29 | all 30 | True 31 | 4600 32 | True 33 | True 34 | True 35 | 0 36 | 6 37 | 0 38 | 40 39 | True 40 | False 41 | False 42 | False 43 | False 44 | 0 45 | 0 46 | False 47 | False 48 | False 49 | False 50 | 0 51 | False 52 | False 53 | False 54 | False 55 | False 56 | False 57 | Species 58 | False 59 | 3 60 | False 61 | True 62 | False 63 | True 64 | False 65 | False 66 | 67 | 68 | 69 | 7 70 | 0.01 71 | 1 72 | 1 73 | 0.01 74 | 8 75 | 25 76 | True 77 | 1 78 | 1 79 | 0 80 | False 81 | True 82 | False 83 | 84 | 2 85 | True 86 | 87 | Oxidation (M) 88 | Acetyl (Protein N-term) 89 | 90 | 0 91 | 0 92 | 25 93 | 15 94 | 0 95 | 1 96 | 97 | 98 | 200 99 | True 100 | True 101 | True 102 | True 103 | True 104 | True 105 | True 106 | False 107 | False 108 | True 109 | False 110 | True 111 | False 112 | 0 113 | 20 114 | 115 | none 116 | False 117 | session1 118 | 1.6.3.3 119 | 120 | 121 | 1 122 | 123 | 124 | 125 | 126 | -1.79589544172745E+308 127 | 1.79589544172745E+308 128 | False 129 | False 130 | False 131 | True 132 | False 133 | False 134 | False 135 | 136 | C:\Raw Files\Sonnett_F1\TGR_02118.raw 137 | C:\Raw Files\Sonnett_F1\TGR_03302.raw 138 | C:\Raw Files\Sonnett_F1\TGR_03303.raw 139 | 140 | 141 | 142 | 143 | 144 | 145 | 146 | 32767 147 | 32767 148 | 32767 149 | 150 | 151 | False 152 | False 153 | False 154 | 155 | 156 | 0 157 | 0 158 | 0 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 0 168 | 7 169 | 2 170 | False 171 | False 172 | True 173 | 1 174 | NaN 175 | NaN 176 | MatchFromAndTo 177 | 0 178 | 8 179 | True 180 | 35 181 | True 182 | 1.4 183 | 1.2 184 | False 185 | 0 186 | 187 | 188 | 189 | Reporter ion MS2 190 | False 191 | 0 192 | False 193 | 3 194 | 6 195 | 100000 196 | 0 197 | 0 198 | False 199 | False 200 | True 201 | False 202 | 2 203 | 0 204 | 5 205 | 2 206 | 1 207 | 0 208 | 0 209 | 0 210 | 0 211 | 212 | 213 | 214 | Trypsin/P 215 | 216 | 217 | 218 | 0 219 | False 220 | False 221 | 222 | Oxidation (M) 223 | Acetyl (Protein N-term) 224 | 225 | False 226 | 227 | 228 | 229 | 230 | TMT10plex-Lys126C 231 | TMT10plex-Nter126C 232 | 0 233 | 0 234 | 0 235 | 0 236 | True 237 | 238 | 239 | TMT10plex-Lys127N 240 | TMT10plex-Nter127N 241 | 0 242 | 0 243 | 0 244 | 0 245 | True 246 | 247 | 248 | TMT10plex-Lys127C 249 | TMT10plex-Nter127C 250 | 0 251 | 0 252 | 0 253 | 0 254 | True 255 | 256 | 257 | TMT10plex-Lys128N 258 | TMT10plex-Nter128N 259 | 0 260 | 0 261 | 0 262 | 0 263 | True 264 | 265 | 266 | TMT10plex-Lys128C 267 | TMT10plex-Nter128C 268 | 0 269 | 0 270 | 0 271 | 0 272 | True 273 | 274 | 275 | TMT10plex-Lys129N 276 | TMT10plex-Nter129N 277 | 0 278 | 0 279 | 0 280 | 0 281 | True 282 | 283 | 284 | TMT10plex-Lys129C 285 | TMT10plex-Nter129C 286 | 0 287 | 0 288 | 0 289 | 0 290 | True 291 | 292 | 293 | TMT10plex-Lys130N 294 | TMT10plex-Nter130N 295 | 0 296 | 0 297 | 0 298 | 0 299 | True 300 | 301 | 302 | TMT10plex-Lys130C 303 | TMT10plex-Nter130C 304 | 0 305 | 0 306 | 0 307 | 0 308 | True 309 | 310 | 311 | TMT10plex-Lys131N 312 | TMT10plex-Nter131N 313 | 0 314 | 0 315 | 0 316 | 0 317 | True 318 | 319 | 320 | TMT11plex-Lys131C 321 | TMT11plex-Nter131C 322 | 0 323 | 0 324 | 0 325 | 0 326 | True 327 | 328 | 329 | 330 | 331 | 332 | 333 | False 334 | 335 | 336 | 337 | 338 | True 339 | 20 340 | 4.5 341 | True 342 | 2 343 | True 344 | 0.6 345 | 0.6 346 | True 347 | True 348 | False 349 | 70 350 | False 351 | 352 | 0 353 | 0 354 | 0 355 | 0.02 356 | 0 357 | False 358 | 0 359 | 0 360 | 0 361 | 0 362 | 0 363 | 0 364 | True 365 | False 366 | True 367 | False 368 | 369 | 0 370 | 6 371 | False 372 | 0 373 | 0 374 | 0 375 | 0 376 | False 377 | 378 | 379 | 380 | 381 | PeptidesWithCleavedLinker 382 | False 383 | True 384 | 385 | 386 | 387 | 388 | FTMS 389 | 20 390 | True 391 | 7 392 | True 393 | 10 394 | True 395 | True 396 | 12 397 | 100 398 | True 399 | True 400 | True 401 | True 402 | False 403 | 404 | 405 | ITMS 406 | 0.5 407 | False 408 | 0.15 409 | False 410 | 0.25 411 | False 412 | False 413 | 8 414 | 100 415 | True 416 | True 417 | True 418 | True 419 | False 420 | 421 | 422 | TOF 423 | 40 424 | True 425 | 0.01 426 | False 427 | 0.02 428 | False 429 | True 430 | 10 431 | 100 432 | True 433 | True 434 | True 435 | True 436 | False 437 | 438 | 439 | Unknown 440 | 0.5 441 | False 442 | 0.15 443 | False 444 | 0.25 445 | False 446 | False 447 | 8 448 | 100 449 | True 450 | True 451 | True 452 | True 453 | False 454 | 455 | 456 | 457 | 458 | CID 459 | False 460 | 1 461 | 1 462 | 1 463 | False 464 | 1 465 | KRH 466 | 467 | 468 | HCD 469 | False 470 | 1 471 | 1 472 | 1 473 | False 474 | 1 475 | KRH 476 | 477 | 478 | ETD 479 | False 480 | 1 481 | 1 482 | 1 483 | False 484 | 1 485 | KRH 486 | 487 | 488 | PQD 489 | False 490 | 1 491 | 1 492 | 1 493 | False 494 | 1 495 | KRH 496 | 497 | 498 | ETHCD 499 | False 500 | 1 501 | 1 502 | 1 503 | False 504 | 1 505 | KRH 506 | 507 | 508 | ETCID 509 | False 510 | 1 511 | 1 512 | 1 513 | False 514 | 1 515 | KRH 516 | 517 | 518 | UVPD 519 | False 520 | 1 521 | 1 522 | 1 523 | False 524 | 1 525 | KRH 526 | 527 | 528 | Unknown 529 | False 530 | 1 531 | 1 532 | 1 533 | False 534 | 1 535 | KRH 536 | 537 | 538 | 539 | --------------------------------------------------------------------------------